(Written as a response to a friend who asked for some thoughts about the article. My, did I ever have thoughts!)

Hi Liz;
As you probably had guessed, I am quite critical about both this article and the ideas it presents. The short version is that I think the ideas are scientifically problematic, the rhetorics is full of fallacies to an extent that makes it close in on dishonesty. I will try to split up my criticisms in categories, although there is an overlap so it’s not always obvious, in which category a point belongs. The categories are:

Rhetorics

Science

Aesthetics

Rhetorics

The author of the article is using a lot of cheap rhetorical tricks which basically serve to manipulate the reader/listener without directly lying. I will try to mention a few of them, but there are many, and I cannot do them all. This doesn’t invalidate the ideas themselves, of course – I haven’t read the original book, and an article should in principle not reflect badly on the book that is its subject. But it still rubs me the wrong way – if the idea was really that good, they shouldn’t need cheap tricks to sell it.

The tricks are quite typical across many groups that try to leech on the perceived authority of science to sell their ideas, including but not limited to creationists.

The first sentence says that the book has “stirred up the Internet”, whatever that even means. Nothing is said, but it is clear from the sentence that apparently this is a very important book with a strong impact (although I have never heard of it before).

It is worth noting that while the whole idea here circles around quantum mechanics, Robert Lanza is not a physicist, but a biologist. I have no doubt that his stem cell research is both important and ground breaking. But that doesn’t make him an expert in quantum physics – if he’s anything like the biologists I have met, his grasp of quantum physics will be only slightly better than that of an educated layperson. Still, the article stresses over and again that he is a scientist, and even the (to this topic) completely irrelevant fact that he has been named the 3rd most important scientist alive by the NYT. Adds to this feeling that they’re trying to sell me something, and something that apparently isn’t good enough to merit its own sales pitch.

The fact that they call his theories “controversial” also sets me off. That is the pseudo scientists’ favorite euphemism for “generally disregarded by the greater Science community as an insult to Science”. It lends the idea an air of danger and edginess that it doesn’t deserve.

Claiming that the astrophysicists that support one of the many Multiverse theories are “unwitting” supporters of Lanza’s ideas isplain and downright dishonest. Lanza’s idea of an immaterial consciousness travelling between Universes does by no means follow directly from any of the theories of multiverses or parallel Universes. It is simply another attempt of trying to leech on the established authority of Scientists in order to sell a point that apparently really cannot stand by itself. This is definitely a low point in the article’s rhetorics, though it never reaches any appreciable heights.

Generally, it there is a tendency of citing different people as just “scientists” without mentioning if they are talking within their field of expertise or not. Thing is, with science – it doesn’t matter who says something. Science is a method that, if applied correctly, will give the same result no matter who does it. On the other hand, no scientist, no mater how much of a genius, is automatically correct simply due to his or her former track record. The only thing that matters is whether they apply the scientific method correctly here and now. The article generally sweeps this under the rug and just goes with the tired old “whoooooaaa, scientist!” trope to lend their idea an air of believability (if that is even a word).

Science

“God of The Gaps”

It seems like the science case here is beating the old creationist horse: if we cannot explain it, then it must be God (or whatever pet deity or spiritual force they are trying to peddle). A special case of the well-known “if I can find the tiniest hole in your explanation, then mine, however preposterous, is automatically true”. The argument is sometimes called the “God of the gaps”, because such a God or spiritual entity or principle can only exist in the cracks left behind by Science, and is thus doomed to a life of eternal retreat as Science advances – a both scientifically and spiritually poor construct.

Lanza’s chosen point of attack is a very popular for pseudoscientists, the so-called fine-tuning problem of Cosmology. The problem is, as it also says in the article, that with our current knowledge, it seems that our Universe, out of all the possible configurations that the laws of nature and the values of the natural constants could have had, it has taken an almost infinitely improbable combination that allows for life to exist. Not the only one, but one out of very, very few compared to the vast number of possible configurations that could not have allowed Life to develop. It is indeed a deep, interesting and profound problem and doesn’t seem to be anywhere near a solution. But Lanza’s and/or the article author’s solution is less than impressive:

Lanza points to the structure of the universe itself, and that the laws,
forces, and constants of the universe appear to be fine-tuned for life,
implying intelligence existed prior to matter.

…Now there’s some jumping to conclusions for ya. I can see no way in which the fact that the universe appears to be fine-tuned should in any way logically imply that intelligence or consciousness should have existed prior to matter.

Among the problems are:

The keyword here is “appears”. The problem arises in a field where we know, that our theories are incomplete. Cosmology (the science of the beginnings and very early eras of the Universe) is an overlap between the theories of Quantum Field Theory and Einstein’s good ol’ General Theory of Relativity – two theories that are both incredibly successful within each their jurisdiction but that are also known to be mutually incompatible. I.e., in their current forms, they cannot both be true at the same time. But they both pass all tests so far with flying colors, so they both are, in some sense, true. Therefore, it is clear that our theories are not complete. But it is exactly according to these theories that the Universe seems fine-tuned. So it would probably be a good idea to remember that “appears” in this case does definitely not mean “certainly is”.

The Fine-tuning argument has another problem. It is appealing to say that “our presence in the Universe is so incredibly improbably that it simply cannot be a result of pure chance”. However, if the Universe had taken on any of the configurations that would not have allowed life to exist, we wouldn’t have been around to observe it! So given the knowledge that we are here to ponder how the Universe works, the probability of being in one of the life-permitting configurations of the Universe is not infinitely small, it is in fact 100%. This argument is pretty weak both ways, though. But it should be a word of caution before concluding too much based on perceived (im-)probabilities.

The Universe is big. Possibly infinite in extent. If it turns out that all the numbers that Lanza talk about are allowed to change, and the Universe really is infinite (or just big enough), then all possible combinations of these numbers will be covered somewhere in the Universe, and we will suddenly be certain to have regions of the Universe that can sustain Life. There is an entire family of theories that operate with this exact idea – so it is not like there are no proposed solutions to the fine-tuning problem out there, it is just that we cannot tell if the ones we have work, and which ones are better.

“Quantum Babble”

“Quantum Babble” is a quite popular genre among pseudoscientists, known from works like “What The Bleep”, “The Secret” and other far from scientific works – often inspired by, but bearing little resemblance to, eastern Buddhism. And although it is not as bad as I have seen it before, this article is definitely rife with quantum babble tropes.

In quantum mechanics, a system is allowed to exist in more different states at the same time (like Schrödingers famous cat that is both dead and alive at the same time), and only “chooses” one of the states once an observation, or measurement, is made. Many Quantum Babblers have taken this to mean that the observer is literally shaping and creating the Universe by his or her own consciousness and thought patterns, and have from here leapt to the conclusion that if we just think the right things, our mind can shape the Universe into anything we want it to – what Barbara Ehrenreich expressed as “basically the notion that wishful thinking works”.

But “the observer” in quantum mechanics is merely a mathematical or conceptual convenience – a cute name for our ignorance. The thing is, we don’t know what it is that triggers this collapse into one of the multiple states of a system – it clearly happens all the time, also when no human is looking. But it definitely happens when we are looking, and therefore it was convenient to use the phrase “an observation” or “a measurement” about any of these processes where this happens. Taking this metaphor too literally simply shows that one has a very limited understanding of quantum physics and doesn’t exactly reinforce my trust in either of these people’s understanding of the science whose name they claim.

Further down, it says:

The triggering factor for these multiplyingworlds is our actions, explained
Everett. If we make some choices, instantly one universe splits into two with
different versions of outcomes

This is simply not true. Or, rather – it is, but that is just because all situations in which we as people make a choice all fall into the category of situations in which an “observation” in the quantum mechanical sense of the word is made. It is simply not true that our mind or consciousness should play any kind of privileged role in this game – all these new Universes branching off of our current one happens all the time (provided the theory is correct, which is far from certain), whether we are around to make a choice on behalf of Nature or not.

The Quantum Soul

While all of us have each our own idea about how the Soul works, nobody has a very clear idea about what it is. To a scientist, however, it must almost by definition be something material, simply because “material” in the broad scientific sense of the word means “something we can observe to exist independent of who conducts the observation”. It is really not a strong requirement to make. If something has any impact on the world, then this thing is, according to this definition, material itself. Even the elusive property of the world called Entropy is “material”. Information is “material”. Therefore, claiming the soul to be “immaterial” pretty much amounts to saying “it has no impact on the Universe whatsoever”. When someone then, as the next step, claims this “immaterial” thing to be the foundation upon which the entire Universe rests, I begin to suspect that these people only have a vague idea about what it is they are talking about.

Their favorite analogy to this soul as something somehow outside of the Universe dropping by for a visit is the electrical pulse in a cable. But this analogy is also fundamentally flawed; the electrical impulse does not have an existence outside and independent from the medium it moves through. It is an emergent phenomenon deeply rooted in the physical substrate through which it moves, owing its existence entirely to the properties of the cable in which it runs and whatever processes outside of the cable – but very much in the same Universe and reality as the cable – that created it.

I don’t know for sure what the Soul is. But I am very convinced that the Soul is also some kind of emergent phenomenon, deeply rooted in and owing its existence to the material substrate – our bodies – in which it lives. That is of course no proof of anything, but the alternative is souls somehow living either outside of Reality (and that doesn’t even make sense to me), or somehow flying around in the world, going from body to body but not leaving any trace between each visit, does – apart from some practical problems – clash with the principle of “Occam’s Razor”, which states that out of two explanations which equally well explain a phenomenon, one should favor the one that requires the fewer, less complex assumptions. Clearly, a Soul which emerges from the substrate in which it sits, and perishes with it (until, maybe, one day we learn to migrate it into something more long-lived) requires fewer assumptions than a soul that is dependent on the brain in which it lives until it somehow can travel around the world, wherever it wants, with no explanation as to how, for as long as it takes, before moving into another body bringing no trace of where it was living before.

One of their strongest cards in the appeal-to-authority game is the ideas of Roger Penrose (although it is not clear whether Penrose actually agrees that his ideas support those of Lanza). While Roger Penrose is a renowned mathematician and great writer, he is a, well, disputed physicist with more imagination than scientific rigor, and he is definitely not either a psychologist, a neurologist or a microbiologist. Which is to say that again, his knowledge of the human mind is not necessarily much stronger than those of the educated layperson. So his ideas about the “quantum information” of the mind somehow being “released” into the Universe when we die without being destroyed, sounds less than convincing to me. Quantum Information is simply another name for the information about the state of a given system. Obviously, this information can be translated to (very complex) math and thus transported somehow – but where, and through what, and where would this information be stored? I don’t even see an attempt at hand-waving explanations here, just claims. And, what is worse, how could quantum information in any meaningful way precede the matter which it describes?

Human exceptionalism

Another thing I don’t like about the whole family of ideas that deal with “consciousness” as if it were having an existence on its own is how it is rooted in the idea that humans should somehow be elevated above the animals, separated from them by this semi-magical property of “consciousness” or a “soul”. If animals have no soul, are they then no more than complicated wind-up toys? If not, at which stage of brain development is it that an animal is rewarded with a soul (as opposed to a mind, which is a property of its and our brain)? Is it birds? Slugs? Dogs? Ants? And why don’t we see an enormous gap between the soul-blessed and the soulless animals in terms of complexity, intelligence and general level of self/reflection and awareness?

Aesthetics

There are other problems about the article, but I am getting very tired now and should go to bed. I just want to end with one more quote from the article:

This account of quantum consciousness explains things like near-death
experiences, astral projection, out of body experiences, and even
reincarnation without needing to appeal to religious ideology.

I would claim that the idea is religious ideology, of a pretty poor, run-of-the-mill pseudoscientific kind, although it is more consistent and thoroughly constructed than most of its kind. Most of the ideas seem unlikely at best, and the whole thing is soaked in misconceptions, hasty conclusions, hand waving and loose, unsupported claims. Generally, where there is some scientific backing, it looks very much like it is cherry-picked to support the already-decided conclusion, rather than basing the conclusion on the evidence.

And again: if the idea were so great, why would they need sensationalist claims and tired old, manipulative rhetorical tricks to sell it?

Disclaimer: I am new to git. I am definitely not an expert. I am a doctoral candidate just learning, and posting this as a reference for myself and, hopefully, as a helpful guide for other beginners. But this is far from exhaustive, and I may even inadvertedly introduce some bad practice.
In fact, recent studies have shown that you will get marmelade on your shirt just before leaving for an important interview if you follow my advise too uncritically.

As the amount, length and complexity of the code I am writing has started to grow, the trusty old copy the entire work folder and continue working on the new copy every time you made a major improvement to your code so you don’t mess it up too bad -approach seems to be more and more uncool. Clumsy, risky, taking up insane amounts of space when there’s also data files etc. to keep track of. So, I decided to see what that version control hype was all about. Maaan, I so should have done that earlier.

Part I: Simple version control/change tracking on a workstation

My user case

I am, a Ph.D. student in astronomy, generally writing code to analyze my data. I work on a university desktop running Ubuntu (but this HowTo should also work just fine on a Mac). I have a laptop also running Ubuntu that I occasionally use to work on my stuff from home. A remote SSH connection is usable but often slow and frustrating, and it’s vulnerable to network outages that sometimes happen on my wireless network.

I want to keep track of changes in my working directory (one for each project I am working on that I want to keep track of independently), I want to be able to perform crazy experiments with my code without having to worry about messing up my stable working version, and I want to be able to synchronize the versions on my home and office computer.

There may very well be other grand and righteous versioning systems out there, I chose Git for the following reasons:

It seems to be very popular, also among grand-scale projects like e.g. the Linux kernel

It is scalable – while it can manage huge and complex projects, my typical small and simple project is quick and easy to set up.

It is flexible: I don’t need a central server to set it up. Any folder on my machine can act as a Git repository. I can synchronize a folder between my office desktop and my private laptop. And should I change my mind and want to set up a full-fledged shared repository on an online server, it is easy to migrate.

Installation and setup

Install

On Linux, Git is very likely found in your package manager. On Ubuntu, install the package from the Software Center or through the Terminal:

$ sudo aptitude install git-core

…that should be it. On a Mac, you can install it from here, or through MacPorts, where it is easy as:

$ sudo port install git-core

– provided you have MacPorts set up already. I’m sure Windows users can install it too, but I have no idea how as I have not been using Windows for work purposes for a very long time.

Personalize

This step is not strictly necessary now, but it will be if you are going to collaborate on a project at a later stage, and it’s easy so just as well just get it over with.

And hey! You can set up a name for your current repo only by omitting the ‘–global‘ option. That way, your info will be remembered only by the repository you are currently working on.

Setting up and maintaining a local repository

Setting up any local directory – that is, any folder on your computer – as a git repository is easy. It does not provide synchronization (yet), but it allows you to track changes to your work and revert to any earlier stage if you’d want to, and to switch between stable and experimental branches. If you want to, it is easy to add more functionality later.

Creating repository from scratch

Let’s start by creating a new folder for our fictional project. Open the terminal, go to the folder where you want to create your project. Now we’ll create a folder, navigate into it, initiate an empty repository and tell Git to add the current folder to the list of files and folders to track:

$ mkdir Gittest
$ cd Gittest
$ git init
$ git add .

Adding files & folders

Git needs to be told specifically which files to track. It is fully possible to have a bunch of untracked files in your repository. So let us create and add a file, e.g. a(n empty) Python-script:

Turning existing project into Git repository

This is very easy, thanks to the fact that Git automatically adds all contents of a folder if you add the folder. So suppose you have a folder where you already have a bunch of subfolders and files, and you want to set it up as a Git repository. Just navigate to it and do the same as before: $ git init $ git add . Git is now tracking all files in the folder and any subfolders. Remember, though, that if you add any folders and files later, you still need to specifically add these before they are tracked.

First snapshot

After you have run the above steps, it is time to make the first snapshot of the new repository. This is done by running:

$ git commit

This opens a text editor – in this case Vim – and prompts you to write a commit message to describe the changes made since last commit; see below. Write the message, save the file and exit the editor.

The current state of your tracked files is now saved with a unique, auto-generated name tag. Snapshots can be taken as often as one wants.

Staging and committing

Git keeps track of your files, but it does not keep track of every little change you make (this is for you to be able to commit changes to one file while holding back changes to another file). Every time you make a commit, you need to stage your changes – that is, to specify which files and changes to include by using ‘git add’ as described above. A shortcut to commit all changes you’ve made to already tracked files, and to avoid the editor opening, is:

$ git commit -a -m "Commit message"

If you want to see which changes are staged and which are not, you can run

$ git status

The command

$ git reset

clears all changes – staged or non-staged – you have made since the last commit.

In practice, I hardly ever worry about staged and unstaged changes, as mostly I just commit with the -a option. But there are times when it comes in handy.

Branching and merging

Suppose you have a piece of code that works and is stable and you need to use it on a regular basis, but on the other hand you really want to add this awesome experimental feature to it. The answer is to create a new branch that we can call e.g. ‘experimental’:

$ git branch experimental

This new branch is basically a safe playground to conduct all the crazy experiment you could think of without ruining anything. To move to the new experimental branch, do:

$ git checkout experimental
$ git branch

The latter git branch with no argument shows you which branches exist, and marks the current branch with an asterisk (‘*‘). All changes made now will be tracked in the experimental branch while leaving the ‘master’ branch alone. If you want to quickly fix a bug in your master branch, you run ‘git checkout master’, modify your code, commit the changes and run ‘git checkout experimental’. This way, you can track changes to two different versions of your code.

I’ll get back to that… (Stashing)

Suppose you are hacking away on your experimental branch. You have made changes to a couple of files, maybe only staged one for commit. It’s all one big, happy creative mess, absolutely not ready for a commit just about now – when you find out you need to fix a simple but important bug in the stable master branch. For situations like this, git has the ‘stash’ command:

$ git stash

This will save the status of your files and changes and “put them aside” for later while reverting the current branch to what it was after the last commit. So say you have added three lines to a file, staged it and than stashed it; you open the file and the three lines are nowhere to be seen. But run

$ git stash apply

and the changes will be back (and can be stashed again etc.). So once you have stashed your changes, you can checkout the master branch, squash that bug, go back to the experimental branch and run run ‘git stash apply’, and your creative mess is back out where it was. Very neat!

Merging

Once that experimental feature is ready to go prime time it is time to merge the ‘experimental’ branch back into ‘master’. With everything staged and committed in the experimental branch, checkout the master branch and run:

$ git merge experimental

Your new awesome feature has now been merged into the master branch, but any bugs you have fixed in master in the meantime of course stay fixed. Notice, though, that while Git is very good at tracking and merging changes, conflicting changes to the same line are marked in the file and will have to be resolved manually.

If your experimental branch is not needed anymore, you can delete it by

$ git branch -d experimental

This requires that there are no changes in the branch that are not merged. If you have this but still want to delete it, force it by using a capital D.

$ git branch -D experimental

Viewing log and restoring old version

To keep track of which changes have been made, you can run

$ git log --graph

The ‘–graph’ option is not necessary but provides the nice illustration of the branching and merging history seen in the left side of thew window.

Undo specific change

As mentioned above, any changes made since the last commit will be cleared with

$ git reset

If you want to undo the effect of a given commit, you find the ID of the commit by running git log and then call:

$ git revert &lt;commit id&gt;

If there are no conflicts, Git can even revert a commit made in the master branch before merging and still keep results of the merging.

Learn more

If this has made you curious to learn more, there is of course a lot of places on the internet that give much more in-depth information about Git. But in fact, Git also has excellent built-in documentation. Try entering

$ git help

in the terminal to see a list of available commends with a short description (there are many more than listed here!), and

$ git help [COMMAND]

to get in-depth information and examples for each of the commands.

In the next post (soon to come), I will write how to keep a synchronized copy of your repository (a clone) on a remote machine. Stay tuned!

The "for the cure" foundation which is against actual cures teams up with a "pro-life" organization to sell life-taking weapons to raise money for the organization that has just announced it is against life-saving. Of course, to perfect the irony, they call it the "Hope Edition".